Table 2

Differences in annotation between manual annotation (MA) and gene build

Replicated transcript in Aedes assembly

Aedes transcript

Supercontig

Contig

Notes

1

1

AAEL013103

1.789

24718

-

-

AAEL014498

1.1137

29191

-

2

AAEL013088

1.789

24718

-

-

AAEL014499

1.1137

29191

-

3

AAEL013092

1.789

24718

-

-

AAEL014500

1.1137

29189

-

4

AAEL013582

1.875

25903

Identical

Longer 5' in MA

AAEL015005

1.1393

31331

5' end of transcript matched MA

AAEL013099

1.789

24718

3' end of transcript matched MA

5*

AAEL015006

1.1393

31331

Identical

-

AAEL013097

1.789

24718

Identical to AAEL013097

AAEL013583

1.875

25903

Identical to AAEL013583

6

AAEL013098

1.789

24719

-

Only 3' coding region lines up

AAEL013098

1.789

24719

Only 3' coding region lines up

3

7*

AAEL009524

1.403

16729

-

-

AAEL000392

1.7

624

-

4

8

AAEL008104

1.301

13837

-

-

-

-

-

-

9

AAEL008110

1.301

13837

Identical

Different intron/exon structure

-

-

-

-

10

AAEL008114

1.301

13837

Identical

3' longer in MA

-

-

-

-

11

AAEL008115

1.301

13837

-

-

-

-

-

-

12

AAEL008103

1.301

13837

Identical

-

-

-

-

-

13

AAEL008100

1.301

13837

-

-

-

-

-

-

5

14*

AAEL014561

1.1166

29449

Identical

-

Transcript missing

1.216

10858

-

15

AAEL014559

1.1166

29447

Identical

-

AAEL006682

1.216

10863

-

6

16*

AAEL014711

1.1232

30069

Identical

Different intron/exon structure

AAEL014491

1.1132

29135

-

17

AAEL014712

1.1232

30070

-

-

AAEL014495

1.1132

29137

-

18

AAEL014709

1.1232

30070

Identical

-

AAEL014494

1.1132

29136

-

7

19

AAEL006423

1.204

10417

-

-

-

-

-

-

20

No transcript

1.204

10417

-

Similar to AAEL003685

-

-

-

-

21*

AAEL006424

1.204

10417

Identical

-

-

-

-

-

22

AAEL006417

1.204

10417

Identical

-

-

-

-

-

8

23*

AAEL006019

1.186

9724

Identical

-

AAEL008297

1.312

14138

-

9

24*

AAEL010573

1.488

18854

Identical

-

AAEL000068

1.1

48

-

25

AAEL010594

1.488

18854

Identical

-

AAEL000046

1.1

48

-

26

AAEL010587

1.488

18855

Identical

-

AAEL000020

1.1

48

-

27

AAEL010575

1.488

18855

Identical

-

AAEL000076

1.1

48

-

28

AAEL000054

1.1

48

-

-

AAEL010578

1.488

18855

-

29

AAEL010595

1.488

18855

-

-

-

-

-

-

10

30

AAEL007897

1.288

13401

Identical

Extra 3' exon in MA

-

-

-

-

31

AAEL007893

1.288

13401

-

-

-

-

-

-

32

AAEL007907

1.288

13401

-

-

-

-

-

-

11

33

AAEL002503

1.59

3864

-

-

-

-

-

-

34

AAEL002532

1.59

3866

Identical

3' exon absent in MA

-

-

-

-

35

AAEL002534

1.59

3863

-

-

-

-

-

-

36

AAEL002523

1.59

3864

-

-

-

-

-

-

12

37

AAEL001205

1.25

1764

-

Longer 5' in MA

-

-

-

-

38

AAEL001215

1.25

1764

Identical

Longer 3' in MA

-

-

-

-

39

AAEL001215

1.25

1764

Identical

-

-

-

-

-

40

AAEL001198

1.25

1761

-

-

-

-

-

-

41

AAEL001201

1.25

1764

-

-

-

-

-

-

42

AAEL001210

1.25

1764

-

-

-

-

-

-

13

43

AAEL008780

1.348

15270

-

-

AAEL001693

1.39

2713

-

44

AAEL008781

1.348

15269

-

-

AAEL001703

1.39

2712

-

45

AAEL008769

1.348

15269

-

-

AAEL001701

1.39

2711

-

46

AAEL008778

1.348

15269

-

-

AAEL001681

1.39

2711

-

14

47

AAEL005065

1.140

7865

-

-

AAEL005223

1.146

8136

-

48

AAEL005085

1.140

7866

-

-

AAEL005220

1.146

8136

-

49

AEL005237

1.146

8136

-

-

AAEL005088

1.140

7865

-

50

AAEL005229

1.146

8136

-

-

AAEL005059

1.140

7865

-

51

AAEL005218

1.146

8136

-

-

No gene build annotation

1.140

7865

-

The 51 manually annotated transcripts (Transcript number) from each BAC clone (BAC
number) along with their corresponding transcript (Gene build transcript) from the
gene build (AaegL1) and their location (supercontig, contig) are listed along with cDNA amplicons if
sequenced. Transcripts that were replicated in the genome are also listed along with
their corresponding gene build transcript, location and differences with the manual
annotation (MA) if any. Manual annotations marked with an asterisk indicate single-copy
cDNA-derived genetic markers used to isolate the BAC.